Preheat the oven to 325°F (165°C).
Season the beef short ribs with salt and pepper.
Heat olive oil in a Dutch oven over medium heat and brown the short ribs on all sides. Remove and set aside.
In the same pot, add onions and cook until caramelized, about 20 minutes.
Add garlic and thyme, cooking for an additional minute.
Deglaze the pot with red wine, scraping up any browned bits.
Return the short ribs to the pot, add beef and chicken broth, and bring to a simmer.
Cover and transfer to the oven. Cook for 2.5 hours, until the ribs are tender.
Remove the ribs, shred the meat, and return it to the pot.
Toast baguette slices and top with grated Gruyere cheese. Broil until melted.
Serve the soup with the cheesy baguette slices on top.